1
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Thompson TQ, O'Leary S, O'Rourke S, Tarsa C, Baerwald MR, Goertler P, Meek MH. Genomics and 20 years of sampling reveal phenotypic differences between subpopulations of outmigrating Central Valley Chinook salmon. Evol Appl 2024; 17:e13705. [PMID: 38832083 PMCID: PMC11146144 DOI: 10.1111/eva.13705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 06/05/2024] Open
Abstract
Intraspecific diversity plays a critical role in the resilience of Chinook salmon populations. California's Central Valley (CV) historically hosted one of the most diverse population complexes of Chinook salmon in the world. However, anthropogenic factors have dramatically decreased this diversity, with severe consequences for population resilience. Here we use next generation sequencing and an archive of thousands of tissue samples collected across two decades during the juvenile outmigration to evaluate phenotypic diversity between and within populations of CV Chinook salmon. To account for highly heterogeneous sample qualities in the archive dataset, we develop and test an approach for population and subpopulation assignments of CV Chinook salmon that allows inclusion of relatively low-quality samples while controlling error rates. We find significantly distinct outmigration timing and body size distributions for each population and subpopulation. Within the archive dataset, spring run individuals that assigned to the Mill and Deer Creeks subpopulation exhibited an earlier and broader outmigration distribution as well as larger body sizes than individuals that assigned to the Butte Creek subpopulation. Within the fall run population, individuals that assigned to the late-fall run subpopulation also exhibited an earlier and broader outmigration distribution and larger body sizes than other fall run fish in our dataset. These results highlight the importance of distinct subpopulations for maintaining remaining diversity in CV Chinook salmon, and demonstrates the power of genomics-based population assignments to aid the study and management of intraspecific diversity.
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Affiliation(s)
- Tasha Q. Thompson
- Michigan State UniversityEast LansingMichiganUSA
- Wild Salmon CenterPortlandOregonUSA
| | - Shannon O'Leary
- Michigan State UniversityEast LansingMichiganUSA
- Saint Anselm CollegeManchesterNew HampshireUSA
| | | | - Charlene Tarsa
- Michigan State UniversityEast LansingMichiganUSA
- Cary Institute of Ecosystem StudiesMillbrookNew YorkUSA
| | | | - Pascale Goertler
- California Department of Water ResourcesSacramentoCaliforniaUSA
- Delta Stewardship CouncilSacramentoCaliforniaUSA
| | - Mariah H. Meek
- Michigan State UniversityEast LansingMichiganUSA
- The Wilderness SocietyBozemanMontanaUSA
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2
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Reis-Santos P, Gillanders BM, Sturrock AM, Izzo C, Oxman DS, Lueders-Dumont JA, Hüssy K, Tanner SE, Rogers T, Doubleday ZA, Andrews AH, Trueman C, Brophy D, Thiem JD, Baumgartner LJ, Willmes M, Chung MT, Charapata P, Johnson RC, Trumble S, Heimbrand Y, Limburg KE, Walther BD. Reading the biomineralized book of life: expanding otolith biogeochemical research and applications for fisheries and ecosystem-based management. REVIEWS IN FISH BIOLOGY AND FISHERIES 2023; 33:411-449. [PMID: 0 DOI: 10.1007/s11160-022-09720-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 07/15/2022] [Indexed: 05/26/2023]
Abstract
AbstractChemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring.
Graphical abstract
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3
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Sorel MH, Murdoch AR, Zabel RW, Kamphaus CM, Buhle ER, Scheuerell MD, Converse SJ. Effects of population density and environmental conditions on life-history prevalence in a migratory fish. Ecol Evol 2023; 13:e10087. [PMID: 37234292 PMCID: PMC10206029 DOI: 10.1002/ece3.10087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/28/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Individual variation in life-history traits can have important implications for the ability of populations to respond to environmental variability and change. In migratory animals, flexibility in the timing of life-history events, such as juvenile emigration from natal areas, can influence the effects of population density and environmental conditions on habitat use and population dynamics. We evaluated the functional relationships between population density and environmental covariates and the abundance of juveniles expressing different life-history pathways in a migratory fish, Chinook salmon (Oncorhynchus tshawytscha), in the Wenatchee River basin in Washington State, USA. We found that the abundance of younger emigrants from natal streams was best described by an accelerating or near-linear function of spawners, whereas the abundance of older emigrants was best described by a decelerating function of spawners. This supports the hypothesis that emigration timing varies in response to density in natal areas, with younger-emigrating life-history pathways comprising a larger proportion of emigrants when densities of conspecifics are high. We also observed positive relationships between winter stream discharge and abundance of younger emigrants, supporting the hypothesis that habitat conditions can also influence the prevalence of different life-history pathways. Our results suggest that early emigration, and a resultant increase in the use of downstream rearing habitats, may increase at higher population densities and with greater winter precipitation. Winter precipitation is projected to increase in this system due to climate warming. Characterizing relationships between life-history prevalence and environmental conditions may improve our understanding of species habitat requirements and is a first step in understanding the dynamics of species with diverse life-history strategies. As environmental conditions change-due to climate change, management, or other factors-resultant life-history changes are likely to have important demographic implications that will be challenging to predict when life-history diversity is not accounted for in population models.
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Affiliation(s)
- Mark H. Sorel
- Washington Cooperative Fish and Wildlife Research Unit, School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | | | - Richard W. Zabel
- Northwest Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AssociationSeattleWashingtonUSA
| | | | - Eric R. Buhle
- Northwest Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AssociationSeattleWashingtonUSA
- Mt. Hood EnvironmentalSandyOregonUSA
| | - Mark D. Scheuerell
- U.S. Geological Survey, Washington Cooperative Fish and Wildlife Research Unit, School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Sarah J. Converse
- U.S. Geological Survey, Washington Cooperative Fish and Wildlife Research Unit, School of Environmental and Forest Sciences & School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
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4
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Munsch SH, Greene CM, Mantua NJ, Satterthwaite WH. One hundred-seventy years of stressors erode salmon fishery climate resilience in California's warming landscape. GLOBAL CHANGE BIOLOGY 2022; 28:2183-2201. [PMID: 35075737 DOI: 10.1111/gcb.16029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 11/12/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
People seek reliable natural resources despite climate change. Diverse habitats and biologies stabilize productivity against disturbances like climate, prompting arguments to promote climate-resilient resources by prioritizing complex, less-modified ecosystems. These arguments hinge on the hypothesis that simplifying and degrading ecosystems will reduce resources' climate resilience, a process liable to be cryptically evolving across landscapes and human generations, but rarely documented. Here, we examined the industrial era (post 1848) of California's Central Valley, chronicling the decline of a diversified, functional portfolio of salmon habitats and life histories and investigating for empirical evidence of lost climate resilience in its fishery. Present perspectives indicate that California's dynamic, warming climate overlaid onto its truncated, degraded habitat mosaic severely constrains its salmon fishery. We indeed found substantial climate constraints on today's fishery, but this reflected a shifted ecological baseline. During the early stages of a stressor legacy that transformed the landscape and -- often consequently -- compressed salmon life history expression, the fishery diffused impacts of dry years across a greater number of fishing years and depended less on cool spring-summer transitions. The latter are important given today's salmon habitats, salmon life histories, and resource management practices, but are vanishing with climate change while year-to-year variation in fishery performance is rising. These findings give empirical weight to the idea that human legacies influence ecosystems' climate resilience across landscapes and boundaries (e.g., land/sea). They also raise the question of whether some contemporary climate effects are recent and attributable not only to increasing climate stress, but to past and present human actions that erode resilience. In general, it is thus worth considering that management approaches that prioritize complex, less-modified ecosystems may stabilize productivity despite increasing climate stress and such protective actions may be required for some ecological services to persist into uncertain climate futures.
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Affiliation(s)
- Stuart H Munsch
- Ocean Associates Inc., Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, USA
| | - Correigh M Greene
- Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, Washington, USA
| | - Nathan J Mantua
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA
| | - William H Satterthwaite
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Santa Cruz, California, USA
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5
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Swimming behavior of emigrating Chinook Salmon smolts. PLoS One 2022; 17:e0263972. [PMID: 35290382 PMCID: PMC8923499 DOI: 10.1371/journal.pone.0263972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 02/01/2022] [Indexed: 11/30/2022] Open
Abstract
Swimming behavior of Chinook Salmon (Oncorhynchus tshawytscha) smolts affects transit time, route selection and survival in complex aquatic ecosystems. Behavior quantified at the river reach and junction scale is of particular importance for route selection and predator avoidance, though few studies have developed field-based approaches for quantifying swimming behavior of juvenile migratory fishes at this fine spatial scale. Two-dimensional acoustic fish telemetry at a river junction was combined with a three-dimensional hydrodynamic model to estimate in situ emigration swimming behavior of federally-threatened juvenile Chinook salmon smolts. Fish velocity over ground was estimated from telemetry, while the hydrodynamic model supplied simultaneous, colocated water velocities, with swimming velocity defined by the vector difference of the two velocities. Resulting swimming speeds were centered around 2 body lengths/second, and included distinct behaviors of positive rheotaxis, negative rheotaxis, lateral swimming, and passive transport. Lateral movement increased during the day, and positive rheotaxis increased in response to local hydrodynamic velocities. Swim velocity estimates were sensitive to the combination of vertical shear in water velocities and vertical distribution of fish.
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6
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Bell-Tilcock M, Jeffres CA, Rypel AL, Willmes M, Armstrong RA, Holden P, Moyle PB, Fangue NA, Katz JVE, Sommer TR, Conrad JL, Johnson RC. Biogeochemical processes create distinct isotopic fingerprints to track floodplain rearing of juvenile salmon. PLoS One 2021; 16:e0257444. [PMID: 34710099 PMCID: PMC8553044 DOI: 10.1371/journal.pone.0257444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/01/2021] [Indexed: 11/18/2022] Open
Abstract
Floodplains represent critical nursery habitats for a variety of fish species due to their highly productive food webs, yet few tools exist to quantify the extent to which these habitats contribute to ecosystem-level production. Here we conducted a large-scale field experiment to characterize differences in food web composition and stable isotopes (δ¹³C, δ¹⁵N, δ³⁴S) for salmon rearing on a large floodplain and adjacent river in the Central Valley, California, USA. The study covered variable hydrologic conditions including flooding (1999, 2017), average (2016), and drought (2012-2015). In addition, we determined incorporation rates and tissue fractionation between prey and muscle from fish held in enclosed locations (experimental fields, cages) at weekly intervals. Finally, we measured δ³⁴S in otoliths to test if these archival biominerals could be used to reconstruct floodplain use. Floodplain-reared salmon had a different diet composition and lower δ13C and δ³⁴S (δ¹³C = -33.02±2.66‰, δ³⁴S = -3.47±2.28‰; mean±1SD) compared to fish in the adjacent river (δ¹³C = -28.37±1.84‰, δ³⁴S = +2.23±2.25‰). These isotopic differences between habitats persisted across years of extreme droughts and floods. Despite the different diet composition, δ¹⁵N values from prey items on the floodplain (δ¹⁵N = 7.19±1.22‰) and river (δ¹⁵N = 7.25±1.46‰) were similar, suggesting similar trophic levels. The food web differences in δ13C and δ³⁴S between habitats were also reflected in salmon muscle tissue, reaching equilibrium between 24-30 days (2014, δ¹³C = -30.74±0.73‰, δ³⁴S = -4.6±0.68‰; 2016, δ¹³C = -34.74 ±0.49‰, δ³⁴S = -5.18±0.46‰). δ³⁴S measured in sequential growth bands in otoliths recorded a weekly time-series of shifting diet inputs, with the outermost layers recording time spent on the floodplain (δ³⁴S = -5.60±0.16‰) and river (δ³⁴S = 3.73±0.98‰). Our results suggest that δ¹³C and δ³⁴S can be used to differentiate floodplain and river rearing habitats used by native fishes, such as Chinook Salmon, across different hydrologic conditions and tissues. Together these stable isotope analyses provide a toolset to quantify the role of floodplains as fish habitats.
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Affiliation(s)
- Miranda Bell-Tilcock
- Center for Watershed Sciences, University of California, Davis, CA, United States of America
| | - Carson A. Jeffres
- Center for Watershed Sciences, University of California, Davis, CA, United States of America
| | - Andrew L. Rypel
- Center for Watershed Sciences, University of California, Davis, CA, United States of America
- Department of Wildlife, Fish & Conservation Biology, University of California, Davis, CA, United States of America
| | - Malte Willmes
- Institute of Marine Sciences, UC Santa Cruz, Santa Cruz, CA, United States of America
- National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, CA, United States of America
| | - Richard A. Armstrong
- Research School of Earth Sciences, Australian National University, Acton, ACT, Australia
| | - Peter Holden
- Research School of Earth Sciences, Australian National University, Acton, ACT, Australia
| | - Peter B. Moyle
- Center for Watershed Sciences, University of California, Davis, CA, United States of America
| | - Nann A. Fangue
- Department of Wildlife, Fish & Conservation Biology, University of California, Davis, CA, United States of America
| | | | - Ted R. Sommer
- Department of Water Resources, West Sacramento, CA, United States of America
| | - J. Louise Conrad
- Delta Stewardship Council, Sacramento, CA, United States of America
| | - Rachel C. Johnson
- Center for Watershed Sciences, University of California, Davis, CA, United States of America
- National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, CA, United States of America
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7
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Michel CJ, Notch JJ, Cordoleani F, Ammann AJ, Danner EM. Nonlinear survival of imperiled fish informs managed flows in a highly modified river. Ecosphere 2021. [DOI: 10.1002/ecs2.3498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Cyril J. Michel
- Institute of Marine Sciences University of California, Santa Cruz Santa Cruz California95060USA
| | - Jeremy J. Notch
- Institute of Marine Sciences University of California, Santa Cruz Santa Cruz California95060USA
| | - Flora Cordoleani
- Institute of Marine Sciences University of California, Santa Cruz Santa Cruz California95060USA
| | - Arnold J. Ammann
- Southwest Fisheries Science Center – Fisheries Ecology Division National Marine Fisheries ServiceNational Oceanic and Atmospheric Administration 110 McAllister Way Santa Cruz California95060USA
| | - Eric M. Danner
- Southwest Fisheries Science Center – Fisheries Ecology Division National Marine Fisheries ServiceNational Oceanic and Atmospheric Administration 110 McAllister Way Santa Cruz California95060USA
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8
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Johnson RC, Stewart AR, Limburg KE, Huang R, Cocherell D, Feyrer F. Lifetime Chronicles of Selenium Exposure Linked to Deformities in an Imperiled Migratory Fish. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2892-2901. [PMID: 32088956 DOI: 10.1021/acs.est.9b06419] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Aquatic ecosystems worldwide face growing threats from elevated levels of contaminants from human activities. Toxic levels of selenium (Se) shown to cause deformities in birds, fish, and mammals can transfer from parents to progeny during embryonic development or accumulate through Se-enriched diets. For migratory species that move across landscapes, tracking exposure to elevated Se is vital to mitigating vulnerabilities. Yet, traditional toxicological investigations resolve only recent Se exposure. Here, we use a novel combination of X-ray fluorescence microscopy and depositional chronology in a biomineral to reveal for the first time provenance, life stage, and duration of toxic Se exposure over the lifetime of an organism. Spinal deformities observed in wild Sacramento Splittail (Pogonichthys macrolepidotus), an imperiled migratory minnow, were attributed to elevated Se acquired through maternal transfer and juvenile feeding on contaminated prey. This novel approach paves the way for diagnosing sources, pathways, and potential for a cumulative exposure of Se relevant for conservation.
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Affiliation(s)
- Rachel Cathleen Johnson
- Fisheries Ecology Division, NOAA Fisheries, Southwest Fisheries Science Center, 110 McAllister Way, Santa Cruz, California 95060, United States
- Center for Watershed Sciences, University of California Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - A Robin Stewart
- Earth System Processes Division, U.S. Geological Survey, 345 Middlefield Road, MS496, Menlo Park, California 94025, United States
| | - Karin E Limburg
- State University of New YorkCollege of Environmental Science and Forestry, 249 Illick Hall, 1 Forestry Drive, Syracuse, New York 13210, United States
| | - Rong Huang
- Cornell High Energy Synchrotron Source, Cornell University, 161 Synchrotron Drive, Ithaca, New York 14850, United States
| | - Dennis Cocherell
- Center for Watershed Sciences, University of California Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Frederick Feyrer
- California Water Science Center, U.S. Geological Survey, 6000 J Street, Placer Hall, Sacramento, California 95819, United States
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9
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Sturrock AM, Carlson SM, Wikert JD, Heyne T, Nusslé S, Merz JE, Sturrock HJW, Johnson RC. Unnatural selection of salmon life histories in a modified riverscape. GLOBAL CHANGE BIOLOGY 2020; 26:1235-1247. [PMID: 31789453 PMCID: PMC7277499 DOI: 10.1111/gcb.14896] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/29/2019] [Indexed: 05/26/2023]
Abstract
Altered river flows and fragmented habitats often simplify riverine communities and favor non-native fishes, but their influence on life-history expression and survival is less clear. Here, we quantified the expression and ultimate success of diverse salmon emigration behaviors in an anthropogenically altered California river system. We analyzed two decades of Chinook salmon monitoring data to explore the influence of regulated flows on juvenile emigration phenology, abundance, and recruitment. We then followed seven cohorts into adulthood using otolith (ear stone) chemical archives to identify patterns in time- and size-selective mortality along the migratory corridor. Suppressed winter flow cues were associated with delayed emigration timing, particularly in warm, dry years, which was also when selection against late migrants was the most extreme. Lower, less variable flows were also associated with reduced juvenile and adult production, highlighting the importance of streamflow for cohort success in these southernmost populations. While most juveniles emigrated from the natal stream as fry or smolts, the survivors were dominated by the rare few that left at intermediate sizes and times, coinciding with managed flows released before extreme summer temperatures. The consistent selection against early (small) and late (large) migrants counters prevailing ecological theory that predicts different traits to be favored under varying environmental conditions. Yet, even with this weakened portfolio, maintaining a broad distribution in migration traits still increased adult production and reduced variance. In years exhibiting large fry pulses, even marginal increases in their survival would have significantly boosted recruitment. However, management actions favoring any single phenotype could have negative evolutionary and demographic consequences, potentially reducing adaptability and population stability. To recover fish populations and support viable fisheries in a warming and increasingly unpredictable climate, coordinating flow and habitat management within and among watersheds will be critical to balance trait optimization versus diversification.
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Affiliation(s)
- Anna M. Sturrock
- Center for Watershed SciencesUniversity of California, DavisDavisCAUSA
| | - Stephanie M. Carlson
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCAUSA
| | | | - Tim Heyne
- California Department of Fish and WildlifeLa GrangeCAUSA
| | - Sébastien Nusslé
- Department of Environmental Science, Policy, and ManagementUniversity of California, BerkeleyBerkeleyCAUSA
| | - Joseph E. Merz
- Institute of Marine SciencesUniversity of California Santa CruzSanta CruzCAUSA
- Cramer Fish SciencesWest SacramentoCAUSA
| | - Hugh J. W. Sturrock
- Department of Epidemiology & BiostatisticsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Rachel C. Johnson
- Center for Watershed SciencesUniversity of California, DavisDavisCAUSA
- Fisheries Ecology DivisionSouthwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
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10
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Brennan SR, Schindler DE, Cline TJ, Walsworth TE, Buck G, Fernandez DP. Shifting habitat mosaics and fish production across river basins. Science 2019; 364:783-786. [PMID: 31123135 DOI: 10.1126/science.aav4313] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/26/2019] [Indexed: 11/02/2022]
Abstract
Watersheds are complex mosaics of habitats whose conditions vary across space and time as landscape features filter overriding climate forcing, yet the extent to which the reliability of ecosystem services depends on these dynamics remains unknown. We quantified how shifting habitat mosaics are expressed across a range of spatial scales within a large, free-flowing river, and how they stabilize the production of Pacific salmon that support valuable fisheries. The strontium isotope records of ear stones (otoliths) show that the relative productivity of locations across the river network, as both natal- and juvenile-rearing habitat, varies widely among years and that this variability is expressed across a broad range of spatial scales, ultimately stabilizing the interannual production of fish at the scale of the entire basin.
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Affiliation(s)
- Sean R Brennan
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA.
| | - Daniel E Schindler
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Timothy J Cline
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Timothy E Walsworth
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Greg Buck
- Alaska Department of Fish and Game, Anchorage, AK 99518, USA
| | - Diego P Fernandez
- Department of Geology and Geophysics, University of Utah, Salt Lake City, UT 84112, USA
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11
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Crozier LG, McClure MM, Beechie T, Bograd SJ, Boughton DA, Carr M, Cooney TD, Dunham JB, Greene CM, Haltuch MA, Hazen EL, Holzer DM, Huff DD, Johnson RC, Jordan CE, Kaplan IC, Lindley ST, Mantua NJ, Moyle PB, Myers JM, Nelson MW, Spence BC, Weitkamp LA, Williams TH, Willis-Norton E. Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem. PLoS One 2019; 14:e0217711. [PMID: 31339895 PMCID: PMC6655584 DOI: 10.1371/journal.pone.0217711] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/16/2019] [Indexed: 12/25/2022] Open
Abstract
Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.
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Affiliation(s)
- Lisa G. Crozier
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
- * E-mail:
| | - Michelle M. McClure
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Tim Beechie
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Steven J. Bograd
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Monterey, California, United States of America
| | - David A. Boughton
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Mark Carr
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, United States of America
| | - Thomas D. Cooney
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Jason B. Dunham
- Forest & Rangeland Ecosystem Science Center, U.S. Geological Survey, Corvallis, Oregon, United States of America
| | - Correigh M. Greene
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Melissa A. Haltuch
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Elliott L. Hazen
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Monterey, California, United States of America
| | - Damon M. Holzer
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - David D. Huff
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Rachel C. Johnson
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
- Center for Watershed Sciences, University of California, Davis, California, United States of America
| | - Chris E. Jordan
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Isaac C. Kaplan
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Steven T. Lindley
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Nathan J. Mantua
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Peter B. Moyle
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, California, United States of America
| | - James M. Myers
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Mark W. Nelson
- ECS Federal, Inc. Under Contract to Office of Sustainable Fisheries, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Silver Spring, Maryland, United States of America
| | - Brian C. Spence
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Laurie A. Weitkamp
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Thomas H. Williams
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Ellen Willis-Norton
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, United States of America
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12
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Friedman WR, Martin BT, Wells BK, Warzybok P, Michel CJ, Danner EM, Lindley ST. Modeling composite effects of marine and freshwater processes on migratory species. Ecosphere 2019. [DOI: 10.1002/ecs2.2743] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Whitney R. Friedman
- Institute of Marine Sciences University of California 100 McAllister Way Santa Cruz California USA
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic Atmospheric Administration 110 McAllister Way Santa Cruz California USA
| | - Benjamin T. Martin
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic Atmospheric Administration 110 McAllister Way Santa Cruz California USA
| | - Brian K. Wells
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic Atmospheric Administration 110 McAllister Way Santa Cruz California USA
| | - Pete Warzybok
- Point Blue Conservation Science Petaluma California USA
| | - Cyril J. Michel
- Institute of Marine Sciences University of California 100 McAllister Way Santa Cruz California USA
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic Atmospheric Administration 110 McAllister Way Santa Cruz California USA
| | - Eric M. Danner
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic Atmospheric Administration 110 McAllister Way Santa Cruz California USA
| | - Steven T. Lindley
- Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service National Oceanic Atmospheric Administration 110 McAllister Way Santa Cruz California USA
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13
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Brennan SR, Cline TJ, Schindler DE. Quantifying habitat use of migratory fish across riverscapes using space‐time isotope models. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13191] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sean R. Brennan
- University of WashingtonSchool of Aquatic and Fishery SciencesSeattle Washington
| | - Timothy J. Cline
- University of WashingtonSchool of Aquatic and Fishery SciencesSeattle Washington
| | - Daniel E. Schindler
- University of WashingtonSchool of Aquatic and Fishery SciencesSeattle Washington
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14
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Dedrick AG, Baskett ML. Integrating Genetic and Demographic Effects of Connectivity on Population Stability: The Case of Hatchery Trucking in Salmon. Am Nat 2018; 192:E62-E80. [PMID: 30016162 DOI: 10.1086/697581] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Connectivity among populations can have counteracting effects on population stability. Demographically, connectivity can rescue local populations but increase the synchrony across populations. Genetically, connectivity can counteract drift locally but homogenize genotypes across populations. Population independence and diversity underlies system-level buffering against environmental variability, termed the portfolio effect. The portfolio effect has declined in California fall-run Chinook salmon, possibly in part because of the trucking of juvenile hatchery-reared fish for downstream release, which reduces juvenile mortality but increases the connectivity between rivers. We use a dynamical population model to test whether this increased connectivity can explain the loss of the portfolio effect and quantify the relative demographic and genetic contributions to portfolio effect erosion. In the model, populations experience different within-population environmental conditions and the same time-variable ocean conditions, the response to which can depend on a quantitative genetic trait. We find that increased trucking for one population's hatchery can lead to a loss of the portfolio effect, with a system-level trade-off between increased average abundance and increased variability in abundance. This trade-off is much stronger when we include the effects of genetic homogenization than when we consider demographic synchronization alone. Therefore, genetic homogenization can outweigh demographic synchrony in determining the system-level effect of connectivity.
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15
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Goertler PAL, Scheuerell MD, Simenstad CA, Bottom DL. Estimating Common Growth Patterns in Juvenile Chinook Salmon (Oncorhynchus tshawytscha) from Diverse Genetic Stocks and a Large Spatial Extent. PLoS One 2016; 11:e0162121. [PMID: 27695094 PMCID: PMC5047595 DOI: 10.1371/journal.pone.0162121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022] Open
Abstract
Life history variation in Pacific salmon (Oncorhynchus spp.) supports species resilience to natural disturbances and fishery exploitation. Within salmon species, life-history variation often manifests during freshwater and estuarine rearing, as variation in growth. To date, however, characterizing variability in growth patterns within and among individuals has been difficult via conventional sampling methods because of the inability to obtain repeated size measurements. In this study we related otolith microstructures to growth rates of individual juvenile Chinook salmon (O. tshawytscha) from the Columbia River estuary over a two-year period (2010-2012). We used dynamic factor analysis to determine whether there were common patterns in growth rates within juveniles based on their natal region, capture location habitat type, and whether they were wild or of hatchery origin. We identified up to five large-scale trends in juvenile growth rates depending on month and year of capture. We also found that hatchery fish had a narrower range of trend loadings for some capture groups, suggesting that hatchery fish do not express the same breadth of growth variability as wild fish. However, we were unable to resolve a relationship between specific growth patterns and habitat transitions. Our study exemplifies how a relatively new statistical analysis can be applied to dating or aging techniques to summarize individual variation, and characterize aspects of life history diversity.
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Affiliation(s)
- Pascale A. L. Goertler
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mark D. Scheuerell
- Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Charles A. Simenstad
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Bottom
- Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
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